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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Oak Ridge National Laboratory Pilot Demonstration of an Attestation and Anomaly Detection Framework using Distributed Ledger Technology for Power Grid Infrastructure

This report summarizes the design and pilot demonstration of a framework called Grid Guard that was created to provide increased data and device trustworthiness to electric grid devices by leveraging distributed ledger technology (DLT), specifically blockchain. Grid Guard contains a combination of core cryptographic methods such as the secure hash algorithm (SHA), and asymmetric cryptography, private permissioned blockchain, baselining configuration data, consensus algorithm (Raft) and the Hyperledger Fabric (HLF) framework. The system implements a low energy, fast, and robust enhancement to system trustworthiness within and across electric grid systems such as substations, control centers and metering infrastructures. Blockchain is a distributed database structured that provides a practically unalterable (immutable) timeline of stored transactions. By relying on hashing and the Raft consensus algorithm, if an entity tries to illegitimately alter a record at one instance of the database the other ledger nodes are not altered. They work to cross-reference each other and easily locate any incorrectly added data and remove it. The bulk raw data is stored in an off-chain storage (outside of the blockchain ledger) and a hash of this baseline data is stored in the Blockchain ledger via hashing windows of time-series and configuration data, after aggregation and filtering. The bulk off-chain data repository is then considered to be trust-anchored using the hashes stored in the blockchain. To secure the electric grid testbed devices and data, device configuration baselines were compared to those baselines that had been previously stored in the ledger. Statistical baselines for device configurations, network communication patterns, and high-speed sensor data are calculated and then stored off-chain and hashes stored in the ledger. Measurements such as three-phase voltage and current, frequency, breaker status, protection scheme settings, network configuration settings (and other device configuration artifacts) and network traffic features (packet interarrival times) are compared every minute or other selected time windows. During phase 1 of the Grid Guard DLT project different DLT technologies were studies, and an assessment was performed on DLT technology vulnerabilities, uses, and key characteristics. DLT consensus protocols were studies (e.g., RAFT, named after Reliable, Replicated, Redundant, And Fault-Tolerant). Also, cryptography, public, private and permissioned or permissionless systems were assessed. Grid Guard implements a permissioned private DLT. Consensus algorithm selection and choice of DLT implementation depended heavily on the use-case. For this use-case, parameters were selected to measure performance and existing tools for assessment. Benchmarking was performed theoretically and practically. During phase 2 hashed transactions/blocks were inserted into the ledger every second. During phase 2 of the Grid Guard DLT project, a prototype framework was developed and demonstrated for attestation of critical substation devices and data using precision timing systems that use PTP and IRIG-B protocols) on a testbed of operational devices that emulated a distribution substation, control center, and power metering infrastructure using real Operational Technology (OT). The testbed includes OT devices such as protective relays, human machine interfaces (HMI), and power meters. To determine when to collect and compare system and network baselines, an initial examination of an anomaly detection capability to identify malicious manipulation of data streams was conducted. The resulting anomaly detection was demonstrated in a set of experiments and leveraged to trigger device artifact attestation checks. Attestation checks occur against device configuration baselines when compared with the immutable blockchain-stored baselines, which provided a cryptographically supported means by which to store baselines. The electrical substation-grid testbed was created to test the Grid Guard framework. The testbed emulates the operations of a portion of a power grid and SCADA systems as closely as possible. The testbed integrates real protocols, mainly IEC 61850 standard protocols, such as the Sampled Value (SV) and the GOOSE protocols. The testbed also supports DNP3 and other layer 2 and layer 3 protocols such as Telnet, SSH, SFTP/FTP and other proprietary protocols needed to connect to industrial control system equipment. The testbed emulates real power conditions using the OpalRT hardware-in-the-loop (HIL) device which can create fault situations that cannot be easily tested on real systems. The electrical substation-grid testbed was created using real measurement, communication, and protection devices that electrical utilities commonly use.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Accelerated epigenetic aging as a risk factor for chronic obstructive pulmonary disease and decreased lung function in two prospective cohort studies

Chronic obstructive pulmonary disease (COPD) is a frequent diagnosis in older individuals and contributor to global morbidity and mortality. Given the link between lung disease and aging, we need to understand how molecular indicators of aging relate to lung function and disease. Using data from the population-based KORA (Cooperative Health Research in the Region of Augsburg) surveys, we associated baseline epigenetic (DNA methylation) age acceleration with incident COPD and lung function. Models were adjusted for age, sex, smoking, height, weight, and baseline lung disease as appropriate. Associations were replicated in the Normative Aging Study. Of 770 KORA participants, 131 developed incident COPD over 7 years. Baseline accelerated epigenetic aging was significantly associated with incident COPD. The change in age acceleration (follow-up – baseline) was more strongly associated with COPD than baseline aging alone. The association between the change in age acceleration between baseline and follow-up and incident COPD replicated in the Normative Aging Study. Associations with spirometric lung function parameters were weaker than those with COPD, but a meta-analysis of both cohorts provide suggestive evidence of associations. Accelerated epigenetic aging, both baseline measures and changes over time, may be a risk factor for COPD and reduced lung function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Evaluation and Validation Approaches for Simulation of Social Behavior: Challenges and Opportunities

While models of social systems have grown in scope to represent increasingly complex phenomena, efforts to validate these models against observations suffer from a number of challenges that include the lack of shared approaches, the use of single-dimensional evaluation criteria, and the difficulty in evaluating causal mechanisms. Moreover, current evaluation approaches suffer from sensitivity of the existing measurements to initial conditions and model assumptions, and failure to account for uncertainty. These effects lead to the lack of generalizability to new contexts, inability to replicate the validation approach for new models, and difficulties in interpretation of validation results. These challenges can be addressed by building a set of diverse and robust evaluation metrics and by developing best practices for comparative, reproducible validation of varied social simulation approaches against real-world data. Herein, we outline several best practices for data-drive model validation, such as defining evaluation strategies consistent with the intended use case and defining broad comparison criteria to highlight both model strengths and weaknesses. Leveraging common validation practices will enable robust analysis of simulation performance across diverse social scenarios and modeling approaches.

Saldanha, Emily G.↗
DOE OSTI2017

Toward Personalized Network Biomarkers in Alzheimer's Disease: Computing Individualized Genomic and Protein Crosstalk Maps

We call for the AD field to move beyond discrete biomarkers and utilize the full power of informatics and big data approaches to build and test personalized markers at a pathway and network level. While we have chosen AD as an example, the issues we propose are also highly relevant to other neurodegenerative disorders, such as vascular dementia or dementia with Lewy bodies, where even less is known about how various biomarkers interact. Indeed, the availability of rich biomarker data across a range of neurodegenerative disorders would enable more accurate pathology-based classification of such conditions (as opposed to the current predominantly clinical classifications). We further hypothesize that building dynamic network biomarkers and pathway crosstalk reference maps using the combined power of several protein/gene-level knowledge priors could accelerate discovery of disease-specific mechanisms and novel drug targets by enrichment with patient specific genetic information. Application of this methodology to large public AD datasets is needed to test our hypotheses and refine the methods. Subsequent replication in independent datasets and population studies as well as functional validation of mechanisms in laboratory models will be the next steps. Ultimately, it is our hope that such novel methods may yield further insights into both disease mechanisms as well as novel targets for biomarker development and drug discovery.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Accelerating discoveries at DIII-D with the Integrated Research Infrastructure

DIII-D research is being accelerated by leveraging high performance computing (HPC) and data resources available through the National Energy Research Scientific Computing Center (NERSC) Superfacility initiative. As part of this initiative, a high-resolution, fully automated, whole discharge kinetic equilibrium reconstruction workflow was developed that runs at the NERSC for most DIII-D shots in under 20 min. This has eliminated a long-standing research barrier and opened the door to more sophisticated analyses, including plasma transport and stability. These capabilities would benefit from being automated and executed within the larger Department of Energy Advanced Scientific Computing Research program’s Integrated Research Infrastructure (IRI) framework. The goal of IRI is to empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation. For transport, we are looking at producing flux matched profiles and also using particle tracing to predict fast ion heat deposition from neutral beam injection before a shot takes place. Our starting point for evaluating plasma stability focuses on the pedestal limits that must be navigated to achieve better confinement. This information is meant to help operators run more effective experiments, so it needs to be available rapidly inside the DIII-D control room. So far this has been achieved by ensuring the data is available with existing tools, but as more novel results are produced new visualization tools must be developed. In addition, all of the high-quality data we have generated has been collected into databases that can unlock even deeper insights. This has already been leveraged for model and code validation studies as well as for developing AI/ML surrogates. The workflows developed for this project are intended to serve as prototypes that can be replicated on other experiments and can be run to provide timely and essential information for ITER, as well as next stage fusion power plants.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1999

Hot Gas Testing Results of Stagnant Volume Filling Through a Back-Filled RSRM Nozzle Joint

Silicone rubber is back-filled into RSW nozzle joints after assembly. A possible artifact of this process is the formation of small pathways through this filter leading to sensitive sealing materials within the joint. At motor ignition, hot gases fill the stagnant volumes within the joint through this path. A series of 14 test has been completed studying this scenario and providing anchoring data for thermal/flow models. Parameters such as gas path cross section, gas path length, gas path materials, fill volume size, and post path gas spreading prior to unpingement on seal material, have been investigated. Tests were accomplished using geometry similar to RSRM nozzle joint 4 with attached volumes replicating the free volume and flow friction in the actual hardware. The test hardware simulated 8 inches of the full-scale circumference. Testing has pointed to changes required in model boundary condition assumptions and gas dynamics corrections for gas paths of this size and geometry. Areas ,where this date has provided improvement in analysis models will be covered as well as model inadequacies that require separate specialized efforts. Questions remaining after this testing and a possible direction for future testing will be suggested.

Prince, Andrew S.↗
NASA NTRS1998

Measuring In-Plane Displacements with Variable Sensitivity Using Diffractive Optic Interferometry

This paper introduces a method called diffractive optic interferometry (DOI) which allows in-plane displacement components to be measured with variable sensitivity. DOI relies on binary optical elements fabricated as phase-type Dammann gratings which produce multiple diffraction orders of nearly equal intensity. Sensitivity is varied by combining the different wavefronts produced by a conjugate pair of these binary optical elements; a transmission element is used to produce several illumination beams while a reflective element, replicated on the surface of a specimen, provides the reference for the undeformed state. The steps taken to design and fabricate these binary optical elements are described. The specimen grating is characterized, and tested on a disk subjected to diametrical compression. Overall, the results are excellent, with experimental data agreeing to within a few percent of the theoretical predictions.

Shepherd, Robert L.↗
NASA NTRS1996

A Comparison of Cloud Microphysical and Optical Properties during TOGA-COARE

The impact of cirrus clouds on climate is an issue of research interest currently. Whether cirrus clouds heat or cool the Earth-atmosphere system depends on the cloud shortwave albedo and infrared reflectance and absorptance. These in turn are determined by the size distribution, phase, and composition of particles in the clouds. The TOGA-COARE campaign presented an excellent opportunity to study cirrus clouds and their influence on climate. In this campaign, a microphysics instrument package was flown aboard the DC-8 aircraft at medium altitudes in cirrus clouds. This package included a 2D Greyscale Cloud Particle Probe, a Forward Scattering Spectrometer Aerosol Probe, and an ice crystal replicator. At the same time the ER-2 equipped with a radiation measurement system flew coordinated flight tracks above the DC-8 at very high altitude. The radiation measurement made were short and long wave fluxes, as well as narrowband fluxes, both upwelling and downwelling. In addition LIDAR data is available. The existence of these data sets allows for a the comparison of radiation measurement with microphysical measurements. For example, the optical depth and effective radius retrieved from the ER-2 radiation measurements can be compared to the microphysical data. Conversely, the optical properties and fluxes produced by the clouds can be calculated from the microphysical measurements and compared to those measured aboard the ER-2. The assumptions required to make these comparisons are discussed. Typical microphysical results show a prevalence of micron-sized particles, in addition to the cloud particles that exceed 100 mm. The large number of small particles or "haze" cause the effective cloud radii to shift to smaller sizes, leading to changes in optical parameters.

Strawa, A. W.↗
DOE OSTI2020

Replicating Machine Learning Experiments in Materials Science

Transparency and reproducibility are important aspects of validation for Machine Learning (ML) models that are not fully understood and applies independently of the application domain.We offer a case study of reproducibility that highlights the challenges encountered when attempting to reproduce analyzes obtained with Machine Learning methods in materials informatics. Our study explores prediction results obtained with ML models and issues in training data serving as input. We discuss challenges related to theory-driven and numerical errors in training data, lack of reproducibility across platforms and versions, and effects of randomness when varying hyperparameters. In addition to model accuracy, a main metric of interest in the ML community, our results show that model sensitivity may be equally important for applying ML in domain applications such a materials science.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

FIRST IMAGES FROM THE FOCUSING OPTICS X-RAY SOLAR IMAGER

The Focusing Optics X-ray Solar Imager (FOXSI) sounding rocket payload flew for the first time on 2012 November 2, producing the first focused images of the Sun above 5 keV. To enable hard X-ray (HXR) imaging spectroscopy via direct focusing, FOXSI makes use of grazing-incidence replicated optics combined with fine-pitch solid-state detectors. On its first flight, FOXSI observed several targets that included active regions, the quiet Sun, and a GOES-class B2.7 microflare. This Letter provides an introduction to the FOXSI instrument and presents its first solar image. These data demonstrate the superiority in sensitivity and dynamic range that is achievable with a direct HXR imager with respect to previous, indirect imaging methods, and illustrate the technological readiness for a spaceborne mission to observe HXRs from solar flares via direct focusing optics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Citizen and machine learning-aided high-resolution mapping of urban heat exposure and stress

Abstract Through conversion of land cover to more built-up, impervious surfaces, cities create hotter environments than their surroundings for urban residents, with large differences expected between different parts of the city. Existing measurements of ambient air temperature and heat stress, however, are often insufficient to capture the intra-urban variability in heat exposure. This study provides a replicable method for modeling air temperature, humidity, and moist heat stress over the urban area of Chapel Hill while engaging citizens to collect high-temporal and spatially-resolved air temperature and humidity measurements. We use low-cost, consumer-grade sensors combined with satellite remote sensing data and machine learning to map urban air temperature and relative humidity over various land-cover classes to understand intra-urban spatial variability of ambient heat exposure at a relatively high resolution (10 m). Our findings show that individuals may be exposed to higher levels of air temperature and moist heat stress than weather station data suggest, and that the ambient heat exposure varies according to land cover type, with tree-covered land the coolest and built-up areas the warmest, and time of day, with higher air temperatures observed during the early afternoon. Combining our resulting dataset with sociodemographic data, policymakers and urban planners in Chapel Hill can use data output from this method to identify areas exposed to high temperature and moist heat stress as a first step to design effective mitigation measures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Results for the Fourth Quarter 2012 Tank 50 WAC Slurry Sample: Chemical and Radionuclide Contaminants

This report details the chemical and radionuclide contaminant results for the characterization of the 2012 Fourth Quarter sampling of Tank 50 for the Saltstone Waste Acceptance Criteria (WAC).1 Information from this characterization will be used by Waste Solidification Engineering (WSE) to support the transfer of low-level aqueous waste from Tank 50 to the Salt Feed Tank in the Saltstone Facility in Z-Area, where the waste will be immobilized. This information is also used to update the Tank 50 Waste Characterization System. The following conclusions are drawn from the analytical results provided in this report: The concentration of the reported chemical and radioactive contaminants were less than their respective WAC Limits and Targets, unless noted in this section. Norpar 13 and Isopar L have higher detection limits 5 compared with the Saltstone WAC 1 . The data provided in this report is based upon the concentrations in the sub-sample, and due to the limited solubility in aqueous solution, may not represent the concentrations of the analytes in Tank 50. Diisooctyl adipate (or diisooctyl hexanedioate) was measured at 1.30E+00 mg/L in one of two replicate measurements conducted on an at-depth sample. a The organic analysis of the at-depth sample was conducted at the request of SRR. 4 This analyte was below the detection limit in the surface sample. The low insoluble solids content increases the measurement uncertainty for insoluble species.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS2019

ESD Reviews: Model Dependence in Multi-Model Climate Ensembles: Weighting, Sub-Selection and Out-Of-Sample Testing

The rationale for using multi-model ensembles in climate change projections and impacts research is often based on the expectation that different models constitute independent estimates; therefore, a range of models allows a better characterisation of the uncertainties in the representation of the climate system than a single model. However, it is known that research groups share literature, ideas for representations of processes, parameterisations, evaluation data sets and even sections of model code. Thus, nominally different models might have similar biases because of similarities in the way they represent a subset of processes, or even be near-duplicates of others, weakening the assumption that they constitute independent estimates. If there are near-replicates of some models, then treating all models equally is likely to bias the inferences made using these ensembles. The challenge is to establish the degree to which this might be true for any given application. While this issue is recognised by many in the community, quantifying and accounting for model dependence in anything other than an ad-hoc way is challenging. Here we present a synthesis of the range of disparate attempts to define, quantify and address model dependence in multi-model climate ensembles in a common conceptual framework, and provide guidance on how users can test the efficacy of approaches that move beyond the equally weighted ensemble. In the upcoming Coupled Model Intercomparison Project phase 6 (CMIP6), several new models that are closely related to existing models are anticipated, as well as large ensembles from some models. We argue that quantitatively accounting for dependence in addition to model performance, and thoroughly testing the effectiveness of the approach used will be key to a sound interpretation of the CMIP ensembles in future scientific studies.

Abramowitz, Gab↗
DOE OSTI2014

SOARCA Peach Bottom Atomic Power Station Long-Term Station Blackout Uncertainty Analysis: Convergence of the Uncertainty Results

This paper describes the convergence of MELCOR Accident Consequence Code System, Version 2 (MACCS2) probabilistic results of offsite consequences for the uncertainty analysis of the State-of-the-Art Reactor Consequence Analyses (SOARCA) unmitigated long-term station blackout scenario at the Peach Bottom Atomic Power Station. The consequence metrics evaluated are individual latent-cancer fatality (LCF) risk and individual early fatality risk. Consequence results are presented as conditional risk (i.e., assuming the accident occurs, risk per event) to individuals of the public as a result of the accident. In order to verify convergence for this uncertainty analysis, as recommended by the Nuclear Regulatory Commission’s Advisory Committee on Reactor Safeguards, a ‘high’ source term from the original population of Monte Carlo runs has been selected to be used for: (1) a study of the distribution of consequence results stemming solely from epistemic uncertainty in the MACCS2 parameters (i.e., separating the effect from the source term uncertainty), and (2) a comparison between Simple Random Sampling (SRS) and Latin Hypercube Sampling (LHS) in order to validate the original results obtained with LHS. Three replicates (each using a different random seed) of size 1,000 each using LHS and another set of three replicates of size 1,000 using SRS are analyzed. The results show that the LCF risk results are well converged with either LHS or SRS sampling. The early fatality risk results are less well converged at radial distances beyond 2 miles, and this is expected due to the sparse data (predominance of “zero” results).

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

Developing a Bubble Chamber Particle Discriminator Using Semi-Supervised Learning

The identification of non-signal events is a major hurdle to overcome for bubble chamber dark matter experiments such as PICO-60. The current practice of manually developing a discriminator function to eliminate background events is difficult when available calibration data is frequently impure and present only in small quantities. In this study, several different discriminator input/preprocessing formats and neural network architectures are applied to the task. First, they are optimized in a supervised learning context. Next, two novel semi-supervised learning algorithms are trained, and found to replicate the Acoustic Parameter (AP) discriminator previously used in PICO-60 with a mean of 97% accuracy.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein

The structure of the SPRY domain of the human RNA helicase DDX1 was determined at 2.0 Å resolution. The SPRY domain provides a putative protein–protein interaction platform within DDX1 that differs from other SPRY domains in its structure and conserved regions. The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein–protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein–protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

NGEE Arctic Plant Traits: Plant Community Composition, Kougarok Road Mile Marker 64, Seward Peninsula, Alaska, 2016

This dataset reports the characteristics of the dominant vegetation communities at the NGEE Arctic Kougarok field site, Kougarok Road Mile Marker 64 on the Seward Peninsula. Selected plots were surveyed from 18-23 July 2016. Environmental data (e.g., elevation, slope, soil moisture regime, disturbance type and degree, mean canopy height, etc.) were also recorded for each plot. Elevation measurements were updated 2020-08-18. All plant species (vascular plants, bryophytes and lichens) were recorded along with their percent cover in the plots as determined visually by the lead author. Plots were chosen subjectively in areas of homogeneous and representative vegetation and varied in size from 1-25 m2 depending on canopy structure and height. The site is an east-facing hillslope with vegetation that varies from the summit to the toeslope. The 30 total plots were selected as five replicate plots sampled from each of the six identified habitat types: 1) non-acidic mountain complex at the hillcrest, 2) dwarf-shrub lichen tundra on the shoulder, 3) alder shrublands predominantly on an elevational band across the backslope, 4) willow-birch tundra on the upper backslope, 5) tussock tundra on the footslope in inter-water tracks, and 6) tussock tundra mixed with willow-birch tundra or alder savanna in poor developed water tracks on the footslope. This dataset is comprised of two comma-separated (*.csv) files containing species and environmental data for the plant community composition plots. It also contains seven zipped folders of plot photographs, one map showing plot locations (*.pdf), one blank datasheet with the key to codes used in the field (*.pdf), select photos organized in a (*.pdf), and one User file (*.pdf). The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

Antibiotic resistance in pathogens is extensively studied, and yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leveraged genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We found that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly, Clostridium difficile strains harboring this gene are at higher abundance in formula-fed infants than C. difficile strains lacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have higher replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism’s direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data to five principal components classified by boosted decision trees. Among the genes involved in predicting whether an organism increased in relative abundance after treatment are those that encode subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics treatment and predict how organisms in the gut microbiome will respond to antibiotic administration.

59 BASIC BIOLOGICAL SCIENCES↗